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Nkya S, Kaywanga F, Nzunda C, Karim S, Solomon D, Saukiwa E, Christopher H, Ngowi D, Johansen J, Urio F, Mgaya J, Chamba C, Hashim F, Ambroise E, Acquah SO, Makani J. Genomics of fetal haemoglobin: a targeted approach for reticulocyte transcriptome study. RESEARCH SQUARE 2023:rs.3.rs-3061395. [PMID: 37461456 PMCID: PMC10350219 DOI: 10.21203/rs.3.rs-3061395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Background Fetal haemoglobin (HbF) remains a major sickle cell disease modifier. The mechanism of HbF synthesis has been studied for several decades with the intention of increasing interventions for sickle cell disease (SCD), including drugs. However, the complex mechanism of HbF synthesis is influenced by multiple genetic factors interacting with environmental factors. In order to capture useful genetic information, especially with limited resources, one has to carefully design the study. This includes choosing the relevant participants, the correct phenotyping, the choice of samples, and the right genomic assays. This paper describes the approach undertaken as part of preparations for a reticulocyte transcriptome study intended to discover genes associated with HbF decline in newborns in Tanzania. Results Of the 152 newborns enrolled in the larger study, 40 babies were selected for the reticulocyte transcriptome study based on their HbF levels at birth and later stage of life. Of these, 30 individuals were included under the category of high HbF levels ranging from 72.6-90% and the remaining 10 under the category of low HbF levels ranging from 5.9 - 10.3%. The reticulocyte enrichment recovery purity ranged from 85% - 97%. The total RNA concentrations obtained were >250 ng total RNA, with the average purity of 1.9 (A 260/280) respectively. The total concentration obtained was sufficient for the transcriptome and other downstream assays. Conclusion We have documented important steps and factors to consider in identifying the relevant participants and required laboratory sample processes prior to the final stage, which involves total reticulocyte RNA sequencing.
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Affiliation(s)
- Siana Nkya
- Muhimbili University of Health and Allied Sciences
| | | | | | | | | | | | | | - Doreen Ngowi
- Muhimbili University of Health and Allied Sciences
| | | | | | | | - Clara Chamba
- Muhimbili University of Health and Allied Sciences
| | | | | | | | - Julie Makani
- Muhimbili University of Health and Allied Sciences
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Bogusławska DM, Skulski M, Bartoszewski R, Machnicka B, Heger E, Kuliczkowski K, Sikorski AF. A rare mutation (p.F149del) of the NT5C3A gene is associated with pyrimidine 5'-nucleotidase deficiency. Cell Mol Biol Lett 2022; 27:104. [PMID: 36434495 PMCID: PMC9700897 DOI: 10.1186/s11658-022-00405-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
Pyrimidine 5'-nucleotidase deficiency is a rare erythrocyte enzymopathy. Here we report two cases of hemolytic anemia in brothers of Polish origin that are associated with a very rare mutation. Heterozygous deletion in the NT5C3A gene (c.444_446delGTT), inherited most likely from their asymptomatic mother, resulted in a single amino acid residue deletion (p.F149del) in cytosolic pyrimidine 5'-nucleotidase. However, only the mutated transcript was present in the reticulocyte transcriptome of both patients. Only residual activity of pyrimidine 5'-nucleotidase in the brothers' erythrocytes could be observed when compared with the controls, including their asymptomatic father and sister. Western blot showed no sign of the presence of 5'-nucleotidase protein in the erythrocytes of both studied patients. The 2.5-fold reduction of the purine/pyrimidine ratio observed only in the brothers' erythrocytes confirms the correlation of the results of molecular analysis, including whole-exome sequencing, with the phenotype of the pyrimidine 5'-nucleotidase deficiency. Altogether, our results may substantiate the hypothesis of the heterogeneity of the molecular basis of the defect involving both the mutation presented here and negative regulation of expression of the "normal" allele.
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Affiliation(s)
- Dżamila M. Bogusławska
- grid.28048.360000 0001 0711 4236Department of Biotechnology, Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1 St., 65-516 Zielona Góra, Poland
| | - Michał Skulski
- grid.8505.80000 0001 1010 5103Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a St., 50-383 Wrocław, Poland
| | - Rafał Bartoszewski
- grid.8505.80000 0001 1010 5103Department of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a St., 50-383 Wrocław, Poland
| | - Beata Machnicka
- grid.28048.360000 0001 0711 4236Department of Biotechnology, Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1 St., 65-516 Zielona Góra, Poland
| | - Elżbieta Heger
- grid.28048.360000 0001 0711 4236Department of Biotechnology, Institute of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1 St., 65-516 Zielona Góra, Poland
| | - Kazimierz Kuliczkowski
- grid.498904.8Silesian Park of Medical Technology Kardio-Med Silesia, M. Curie-Skłodowskiej 10C St., 41-800 Zabrze, Poland
| | - Aleksander F. Sikorski
- Research and Development Centre, Regional Specialist Hospital, Kamieńskiego 73a St., 51-154 Wrocław, Poland
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3
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Moszyńska A, Jaśkiewicz M, Serocki M, Cabaj A, Crossman DK, Bartoszewska S, Gebert M, Dąbrowski M, Collawn JF, Bartoszewski R. The hypoxia-induced changes in miRNA-mRNA in RNA-induced silencing complexes and HIF-2 induced miRNAs in human endothelial cells. FASEB J 2022; 36:e22412. [PMID: 35713587 DOI: 10.1096/fj.202101987r] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 11/11/2022]
Abstract
The cellular adaptive response to hypoxia relies on the expression of hypoxia-inducible factors (HIFs), HIF-1 and HIF-2. HIFs regulate global gene expression changes during hypoxia that are necessary for restoring oxygen homeostasis and promoting cell survival. In the early stages of hypoxia, HIF-1 is elevated, whereas at the later stages, HIF-2 becomes the predominant form. What governs the transition between the two HIFs (the HIF switch) and the role of miRNAs in this regulation are not completely clear. Genome-wide expression studies on the miRNA content of RNA-induced silencing complexes (RISC) in HUVECs exposed to hypoxia compared to the global miRNA-Seq analysis revealed very specific differences between these two populations. We analyzed the miRNA and mRNA composition of RISC at 2 h (mainly HIF-1 driven), 8 h (HIF-1 and HIF-2 elevated), and 16 h (mainly HIF-2 driven) in a gene ontology context. This allowed for determining the direct impact of the miRNAs in modulating the cellular signaling pathways involved in the hypoxic adaptive response. Our results indicate that the miRNA-mRNA RISC components control the adaptive responses, and this does not always rely on the miRNA transcriptional elevations during hypoxia. Furthermore, we demonstrate that the hypoxic levels of the vast majority of HIF-1-dependent miRNAs (including miR-210-3p) are also HIF-2 dependent and that HIF-2 governs the expression of 11 specific miRNAs. In summary, the switch from HIF-1 to HIF-2 during hypoxia provides an important level of miRNA-driven control in the adaptive pathways in endothelial cells.
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Affiliation(s)
- Adrianna Moszyńska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Jaśkiewicz
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Marcin Serocki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - David K Crossman
- Department of Genetics, The UAB Genomics Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
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4
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Yang F, Ruan H, Li S, Hou W, Qiu Y, Deng L, Su S, Chen P, Pang L, Lai K. Analysis of circRNAs and circRNA-associated competing endogenous RNA networks in β-thalassemia. Sci Rep 2022; 12:8071. [PMID: 35577924 PMCID: PMC9110710 DOI: 10.1038/s41598-022-12002-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
The involvement of circRNAs in β-thalassemia and their actions on fetal hemoglobin (HbF) is unclear. Here, the circRNAs in β-thalassemia carriers with high HbF levels were comprehensively analyzed and compared with those of healthy individuals. Differential expression of 2183 circRNAs was observed and their correlations with hematological parameters were investigated. Down-regulated hsa-circRNA-100466 had a strong negative correlation with HbF and HbA2. Bioinformatics was employed to construct a hsa-circRNA-100466‑associated competing endogenous RNA (ceRNA) network to identify hub genes and associated miRNAs. The hsa-circRNA-100466▁miR-19b-3p▁SOX6 pathway was identified using both present and previously published data. The ceRNA network was verified by qRT-PCR analysis of β-thalassemia samples, RNA immunoprecipitation of K562 cell lysates, and dual-luciferase reporter analysis. qRT-PCR confirmed that hsa-circRNA-100466 and SOX6 were significantly down-regulated, while miR-19b-3p was up-regulated. Hsa-circRNA-100466, miR-19b-3p, and SOX6 were co-immunoprecipitated by anti-argonaute antibodies, indicating involvement with HbF induction. A further dual-luciferase reporter assay verified that miR-19b-3p interacted directly with hsa-circRNA-100466 and SOX6. Furthermore, spearman correlation coefficients revealed their significant correlations with HbF. In conclusion, a novel hsa-circRNA-100466▁miR-19b-3p▁SOX6 pathway was identified, providing insight into HbF induction and suggesting targets β-thalassemia treatment.
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Affiliation(s)
- Fang Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Heyun Ruan
- Department of Obstetrics and Gynecology, Minzu Hospital of Guangxi, Zhuang Autonomous Region, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shuquan Li
- NHC Key Laboratory of Thalassemia Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Hou
- NHC Key Laboratory of Thalassemia Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yuling Qiu
- NHC Key Laboratory of Thalassemia Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lingjie Deng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Sha Su
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ping Chen
- NHC Key Laboratory of Thalassemia Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China. .,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China. .,Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Lihong Pang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Ketong Lai
- NHC Key Laboratory of Thalassemia Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China. .,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China. .,Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
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5
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Skulski M, Bartoszewski R, Majkowski M, Machnicka B, Kuliczkowski K, Sikorski AF, Bogusławska DM. Efficient method for isolation of reticulocyte RNA from healthy individuals and hemolytic anaemia patients. J Cell Mol Med 2018; 23:487-496. [PMID: 30450750 PMCID: PMC6307756 DOI: 10.1111/jcmm.13951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/10/2018] [Indexed: 11/30/2022] Open
Abstract
Despite enormous progress and development of high‐throughput methods in genome‐wide mRNA analyses, data on the erythroid transcriptome are still limited, even though they could be useful in medical diagnostics and personalized therapy as well as in research on normal and pathological erythroid maturation. Although obtaining normal and pathological reticulocyte transcriptome profiles should contribute greatly to our understanding of the molecular bases of terminal erythroid differentiation as well as the mechanisms of the hematological diseases, a basic limitation of these studies is the difficulty of efficient reticulocyte RNA isolation from human peripheral blood. The restricted number of possible parallel experiments primarily concern healthy individuals with the lowest number of reticulocytes in the peripheral blood and a low RNA content. In the present study, an efficient method for reticulocyte RNA isolation from healthy individuals and hemolytic anaemia patients is presented. The procedure includes leukofiltration, Ficoll‐Paque gradient centrifugation, Percoll gradient centrifugation, and negative (CD45 and CD61) immunomagnetic separation. This relatively fast and simple four‐stage method was successfully applied to obtain a reticulocyte‐rich population from healthy subjects, which was used to efficiently isolate the high‐quality RNA essential for successful NGS‐based transcriptome analysis.
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Affiliation(s)
- Michał Skulski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Majkowski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Beata Machnicka
- Department of Biochemistry and Bioinformatics, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | - Kazimierz Kuliczkowski
- Department of Haematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Wrocław, Poland
| | - Aleksander F Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dżamila M Bogusławska
- Department of Biochemistry and Bioinformatics, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
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